The 'save to a single file' is no longer an explicit option. However, this is now automatically invoked whenever the input file has not been split into separate tracks. In order to ensure this you simply need to set the 'track detection threshold' to 0 (off). You can do this in Auto-Scan Options before you load a file; or if a file is already loaded, you can use the Waveform - Re-scan Tracks command.

The explicit option was taken out because it was confusing some users especially when there was only a single track being processed.